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Created new schemas for ion channel use case: (#166) (#167)
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* IonChannelGene schema
* Transfection schema
* PatchClamp schema
* HostCell schema
* Cell schema
* TraceCollection schema
* added GeneOntologyTermShape
* added CellLineOntologyTermShape
* created new data context with missing terms
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@annakristinkaufmann @MFSY
annakristinkaufmann authored and MFSY committed Aug 15, 2018
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601 changes: 601 additions & 0 deletions modules/commons/src/main/resources/contexts/neurosciencegraph/core/data/v1.0.4.json
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184 changes: 184 additions & 0 deletions ...src/main/resources/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.3.json
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{
"@context": [
"{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
{
"this": "{{base}}/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.2/shapes/"
}
],
"imports": [
"{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1"
],
"@type": "nxv:Schema",
"shapes": [
{
"@id": "this:SpeciesOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a species",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:ModelSimulationStatusOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a model simulation status",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:SexOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a sex",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:CellTypeOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a cell type",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:ObjectiveTypeOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a microscope objective type",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:BrainRegionOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a brain region",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:StimulusTypeOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a stimulus type",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:EcodeOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing an eCode",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:RoleOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a role",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:LicenseOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a license",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:SomaTypeTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing the types of somas of the reconstructed cell",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:UnitOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a unit code",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:LabelingCompoundOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a labeling compound",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:MorphologicalCellTypeOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a morphological cell type",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:ElectricalCellTypeOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing an electrical cell type",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:CellLineOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a cell line",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
},
{
"@id": "this:GeneOntologyTermShape",
"@type": "sh:NodeShape",
"label": "The shape of an ontology term representing a gene",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.1/shapes/LabeledOntologyEntityShape"
}
]
}
]
}
37 changes: 37 additions & 0 deletions modules/core/src/main/resources/schemas/neurosciencegraph/core/tracecollection/v0.1.0.json
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{
"@context": [
"{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
{
"this": "{{base}}/schemas/neurosciencegraph/core/tracecollection/v0.1.0/shapes/"
}
],
"@type": "nxv:Schema",
"imports": [
"{{base}}/schemas/neurosciencegraph/commons/collection/v0.2.0"
],
"shapes": [
{
"@id": "this:TraceCollectionShape",
"@type": "sh:NodeShape",
"label": "Trace Collection",
"comment": "Trace collection.",
"targetClass": "nsg:TraceCollection",
"and" : [
{
"node" : "{{base}}/schemas/neurosciencegraph/commons/collection/v0.2.0/shapes/CollectionShape"
},
{
"property" : [
{
"path" : "prov:hadMember",
"name" : "Member",
"description" : "The traces that are member of the collection.",
"class" : "nsg:Trace",
"seeAlso" : "{{base}}/schemas/neurosciencegraph/electrophysiology/trace/v1.0.0/shapes/TraceShape"
}
]
}
]
}
]
}
26 changes: 26 additions & 0 deletions modules/experiment/src/main/resources/schemas/neurosciencegraph/experiment/cell/v0.1.0.json
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{
"@context": [
"{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
{
"this": "{{base}}/schemas/neurosciencegraph/experiment/cell/v0.1.0/shapes/"
}
],
"@type": "nxv:Schema",
"imports": [
"{{base}}/schemas/neurosciencegraph/commons/entity/v1.0.0"
],
"shapes": [
{
"@id": "this:CellShape",
"@type": "sh:NodeShape",
"label": "Cell shape definition",
"targetClass": "nsg:Cell",
"nodeKind": "sh:BlankNodeOrIRI",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/entity/v1.0.0/shapes/EntityShape"
}
]
}
]
}
38 changes: 38 additions & 0 deletions ...s/experiment/src/main/resources/schemas/neurosciencegraph/experiment/hostcell/v0.1.0.json
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{
"@context": [
"{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
{
"this": "{{base}}/schemas/neurosciencegraph/experiment/hostcell/v0.1.0/shapes/"
}
],
"@type": "nxv:Schema",
"imports": [
"{{base}}/schemas/neurosciencegraph/commons/entity/v1.0.0",
"{{base}}/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.3"
],
"shapes": [
{
"@id": "this:HostCellShape",
"@type": "sh:NodeShape",
"label": "Host cell shape definition",
"targetClass": "nsg:HostCell",
"nodeKind": "sh:BlankNodeOrIRI",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/entity/v1.0.0/shapes/EntityShape"
},
{
"property": [
{
"path": "nsg:cellLine",
"name": "Cell line",
"description": "The cell line to which the host cell belongs. Cell lines may come fom the cell line ontology: http://www.clo-ontology.org/",
"node": "{{base}}/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.3/shapes/CellLineOntologyTermShape",
"maxCount": 1
}
]
}
]
}
]
}
39 changes: 39 additions & 0 deletions ...riment/src/main/resources/schemas/neurosciencegraph/experiment/ionchannelgene/v0.1.0.json
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{
"@context": [
"{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
{
"this": "{{base}}/schemas/neurosciencegraph/experiment/ionchannelgene/v0.1.0/shapes/"
}
],
"@type": "nxv:Schema",
"imports": [
"{{base}}/schemas/neurosciencegraph/commons/entity/v1.0.0",
"{{base}}/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.3"

],
"shapes": [
{
"@id": "this:IonChannelGeneShape",
"@type": "sh:NodeShape",
"label": "Ion channel gene shape definition",
"targetClass": "nsg:IonChannelGene",
"nodeKind": "sh:BlankNodeOrIRI",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/entity/v1.0.0/shapes/EntityShape"
},
{
"property": [
{
"path": "nsg:ionChannelGene",
"name": "Ion channel gene",
"description": "The ion channel gene. Ion channel genes should come fom the gene ontology: http://www.geneontology.org/",
"node": "{{base}}/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.3/shapes/GeneOntologyTermShape",
"maxCount": 1
}
]
}
]
}
]
}
27 changes: 27 additions & 0 deletions ...experiment/src/main/resources/schemas/neurosciencegraph/experiment/patchclamp/v0.1.0.json
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{
"@context": [
"{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
{
"this": "{{base}}/schemas/neurosciencegraph/experiment/patchclamp/v0.1.0/shapes/"
}
],
"imports": [
"{{base}}/schemas/neurosciencegraph/commons/activity/v0.1.4"

],
"@type": "nxv:Schema",
"shapes": [
{
"@id": "this:PatchClampShape",
"@type": "sh:NodeShape",
"label": "Patch clamp shape definition",
"nodeKind": "sh:BlankNodeOrIRI",
"targetClass": "nsg:PatchClamp",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/activity/v0.1.4/shapes/ActivityShape"
}
]
}
]
}
27 changes: 27 additions & 0 deletions ...periment/src/main/resources/schemas/neurosciencegraph/experiment/transfection/v0.1.0.json
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{
"@context": [
"{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
{
"this": "{{base}}/schemas/neurosciencegraph/experiment/transfection/v0.1.0/shapes/"
}
],
"imports": [
"{{base}}/schemas/neurosciencegraph/commons/activity/v0.1.4"

],
"@type": "nxv:Schema",
"shapes": [
{
"@id": "this:TransfectionShape",
"@type": "sh:NodeShape",
"label": "Transfection shape definition",
"nodeKind": "sh:BlankNodeOrIRI",
"targetClass": "nsg:Transfection",
"and": [
{
"node": "{{base}}/schemas/neurosciencegraph/commons/activity/v0.1.4/shapes/ActivityShape"
}
]
}
]
}
2 changes: 2 additions & 0 deletions provpatterns/assets/ion-channel-trace-recording-prov-template.svg
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